0.026713
0.000000
0.000000
0.000000
0.010555
0.000000
0.000000
0.000000
0.010331
0.00000
0.00000
0.00000
Nolte, R.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
37.435
94.742
96.797
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O3 S
137.158
n
S-HYDROXYCYSTEINE
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C21 H22 N6 O3
406.438
N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine
non-polymer
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
S
N
78
N
C
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
N
N
90
R
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
S
N
95
N
O
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
N
N
104
S
C
N
105
N
C
N
106
N
O
N
107
N
C
N
108
N
C
N
109
N
C
N
110
N
O
N
111
N
N
N
112
N
O
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
N
N
143
N
C
N
144
N
C
N
145
N
O
N
146
N
O
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
N
N
153
S
C
N
154
N
C
N
155
N
O
N
156
N
C
Y
157
N
C
Y
158
N
N
Y
159
N
C
Y
160
N
C
Y
161
N
N
N
162
N
O
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
O
N
174
N
H
N
175
N
H
N
176
N
N
N
177
S
C
N
178
N
C
N
179
N
O
N
180
S
C
N
181
N
C
N
182
N
C
N
183
N
C
N
184
N
O
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
O
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
N
N
221
S
C
N
222
N
C
N
223
N
O
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
N
N
229
N
O
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
N
N
246
S
C
N
247
N
C
N
248
N
O
N
249
N
C
N
250
N
C
N
251
N
S
N
252
N
C
N
253
N
O
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
N
N
266
S
C
N
267
N
C
N
268
N
O
N
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
N
276
N
O
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
O
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
N
N
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
N
317
N
C
N
318
N
C
N
319
N
O
Y
320
N
C
Y
321
N
C
Y
322
N
N
Y
323
N
C
Y
324
N
C
Y
325
N
C
N
326
N
C
Y
327
N
N
Y
328
N
N
Y
329
N
C
Y
330
N
N
Y
331
N
C
N
332
N
O
N
333
N
C
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
N
N
358
S
C
N
359
N
C
N
360
N
O
N
361
N
C
N
362
N
O
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
S
N
372
N
O
N
373
N
O
N
374
N
O
N
375
N
O
N
376
N
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
R
C
N
381
N
O
N
382
N
C
N
383
N
O
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
N
N
394
S
C
N
395
N
C
N
396
N
O
N
397
N
C
Y
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
N
Y
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
N
407
N
O
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
N
N
421
S
C
N
422
N
C
N
423
N
O
N
424
N
C
Y
425
N
C
Y
426
N
C
Y
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
C
N
431
N
O
N
432
N
O
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
N
N
445
S
C
N
446
N
C
N
447
N
O
N
448
N
C
N
449
N
C
N
450
N
C
N
451
N
O
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
doub
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
Y
154
N
sing
Y
155
N
doub
Y
156
N
doub
N
157
N
sing
Y
158
N
sing
N
159
N
sing
Y
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
doub
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
doub
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
doub
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
Y
262
N
doub
Y
263
N
sing
Y
264
N
sing
N
265
N
sing
Y
266
N
doub
N
267
N
sing
Y
268
N
doub
N
269
N
sing
Y
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
Y
295
N
doub
Y
296
N
sing
Y
297
N
doub
Y
298
N
sing
Y
299
N
doub
Y
300
N
sing
Y
301
N
sing
Y
302
N
doub
Y
303
N
doub
Y
304
N
sing
Y
305
N
sing
N
306
N
sing
Y
307
N
doub
Y
308
N
sing
Y
309
N
sing
Y
310
N
doub
Y
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
Y
318
N
doub
Y
319
N
sing
Y
320
N
doub
Y
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
doub
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
doub
N
360
N
doub
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
doub
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
Y
390
N
doub
Y
391
N
sing
Y
392
N
sing
N
393
N
sing
Y
394
N
doub
Y
395
N
sing
Y
396
N
sing
N
397
N
sing
Y
398
N
sing
Y
399
N
doub
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
doub
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
Y
418
N
doub
Y
419
N
sing
Y
420
N
sing
N
421
N
sing
Y
422
N
doub
N
423
N
sing
Y
424
N
doub
N
425
N
sing
Y
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
doub
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
51
4632
4640
10.1021/jm800566m
18620382
Discovery of 5-[[4-[(2,3-dimethyl-2H-indazol-6-yl)methylamino]-2-pyrimidinyl]amino]-2-methyl-benzenesulfonamide (Pazopanib), a novel and potent vascular endothelial growth factor receptor inhibitor.
2008
10.2210/pdb3cjf/pdb
pdb_00003cjf
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2000-03-01
MAR CCD 165 mm
Si111
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
17-ID
APS
1.000
SYNCHROTRON
APS BEAMLINE 17-ID
35491.906
Vascular endothelial growth factor receptor 2
2.7.10.1
kinase domain; residues 806-939 and 994-1168
1
man
polymer
96.063
SULFATE ION
4
syn
non-polymer
406.438
N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine
1
syn
non-polymer
18.015
water
82
nat
water
VEGFR-2, Kinase insert domain receptor, Protein-tyrosine kinase receptor Flk-1, CD309 antigen
no
yes
MDPDELPLDEHCERLPYDASKWEFPRDRLNLGKPLGRGAFGQVIEADAFGIDKTAT(CSO)RTVAVKMLKEGATHSEHRA
LMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKDLYKDFLTLEHLI(CSO)YSFQ
VAKGMEFLASRK(CSO)IHRDLAARNILLSEKNVVKI(CSO)DFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYT
IQSDVWSFGVLLWEIFSLGASPYPGVKIDEEF(CSO)RRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEH
LGNLLQANA
MDPDELPLDEHCERLPYDASKWEFPRDRLNLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSE
LKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKDLYKDFLTLEHLICYSFQVAKGMEFL
ASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIF
SLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
1
KID insert removed
134
KDR, FLK1
Homo sapiens
Spodoptera frugiperda
BACULOVIRUS
human
sample
135
KID insert removed
309
KDR, FLK1
Homo sapiens
Spodoptera frugiperda
BACULOVIRUS
1
2.42
49.14
VAPOR DIFFUSION, HANGING DROP
VAPOR DIFFUSION, HANGING DROP
entity_src_gen
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Advisory
Refinement description
Version format compliance
Source and taxonomy
Refinement description
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2008-10-07
1
1
2011-07-13
1
2
2017-08-23
1
3
2017-10-25
1
4
2023-08-30
1
5
2023-11-15
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
Related structure of the unliganded version of the protein
Crystal structure of vegfr2 in complex with a 2-anilino-5- aryl-oxazole inhibitor
Crystal structure of vegfr2 in complex with a 2-anilino-5- aryl-oxazole inhibitor
Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine
Crystal structure of VEGFR2 in complex with a
3,4,5-trimethoxy aniline containing pyrimidine, KIM
RCSB
Y
RCSB
2008-03-12
REL
REL
SO4
SULFATE ION
SAV
N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine
HOH
water
K -> N CONFLICT IN UNP ENTRY P35968
1VR2
Unliganded Vegfr2 kinase domain solved in house - similar to pdb entry 1VR2
PDB
experimental model
SO4
1
2
SO4
SO4
1
A
SO4
2
2
SO4
SO4
2
A
SO4
3
2
SO4
SO4
3
A
SO4
4
2
SO4
SO4
4
A
SAV
1167
3
SAV
SAV
1167
A
HOH
1168
4
HOH
HOH
1168
A
HOH
1169
4
HOH
HOH
1169
A
HOH
1170
4
HOH
HOH
1170
A
HOH
1171
4
HOH
HOH
1171
A
HOH
1172
4
HOH
HOH
1172
A
HOH
1173
4
HOH
HOH
1173
A
HOH
1174
4
HOH
HOH
1174
A
HOH
1175
4
HOH
HOH
1175
A
HOH
1176
4
HOH
HOH
1176
A
HOH
1177
4
HOH
HOH
1177
A
HOH
1178
4
HOH
HOH
1178
A
HOH
1179
4
HOH
HOH
1179
A
HOH
1180
4
HOH
HOH
1180
A
HOH
1181
4
HOH
HOH
1181
A
HOH
1182
4
HOH
HOH
1182
A
HOH
1183
4
HOH
HOH
1183
A
HOH
1184
4
HOH
HOH
1184
A
HOH
1185
4
HOH
HOH
1185
A
HOH
1186
4
HOH
HOH
1186
A
HOH
1187
4
HOH
HOH
1187
A
HOH
1188
4
HOH
HOH
1188
A
HOH
1189
4
HOH
HOH
1189
A
HOH
1190
4
HOH
HOH
1190
A
HOH
1191
4
HOH
HOH
1191
A
HOH
1192
4
HOH
HOH
1192
A
HOH
1193
4
HOH
HOH
1193
A
HOH
1194
4
HOH
HOH
1194
A
HOH
1195
4
HOH
HOH
1195
A
HOH
1196
4
HOH
HOH
1196
A
HOH
1197
4
HOH
HOH
1197
A
HOH
1198
4
HOH
HOH
1198
A
HOH
1199
4
HOH
HOH
1199
A
HOH
1200
4
HOH
HOH
1200
A
HOH
1201
4
HOH
HOH
1201
A
HOH
1202
4
HOH
HOH
1202
A
HOH
1203
4
HOH
HOH
1203
A
HOH
1204
4
HOH
HOH
1204
A
HOH
1205
4
HOH
HOH
1205
A
HOH
1206
4
HOH
HOH
1206
A
HOH
1207
4
HOH
HOH
1207
A
HOH
1208
4
HOH
HOH
1208
A
HOH
1209
4
HOH
HOH
1209
A
HOH
1210
4
HOH
HOH
1210
A
HOH
1211
4
HOH
HOH
1211
A
HOH
1212
4
HOH
HOH
1212
A
HOH
1213
4
HOH
HOH
1213
A
HOH
1214
4
HOH
HOH
1214
A
HOH
1215
4
HOH
HOH
1215
A
HOH
1216
4
HOH
HOH
1216
A
HOH
1217
4
HOH
HOH
1217
A
HOH
1218
4
HOH
HOH
1218
A
HOH
1219
4
HOH
HOH
1219
A
HOH
1220
4
HOH
HOH
1220
A
HOH
1221
4
HOH
HOH
1221
A
HOH
1222
4
HOH
HOH
1222
A
HOH
1223
4
HOH
HOH
1223
A
HOH
1224
4
HOH
HOH
1224
A
HOH
1225
4
HOH
HOH
1225
A
HOH
1226
4
HOH
HOH
1226
A
HOH
1227
4
HOH
HOH
1227
A
HOH
1228
4
HOH
HOH
1228
A
HOH
1229
4
HOH
HOH
1229
A
HOH
1230
4
HOH
HOH
1230
A
HOH
1231
4
HOH
HOH
1231
A
HOH
1232
4
HOH
HOH
1232
A
HOH
1233
4
HOH
HOH
1233
A
HOH
1234
4
HOH
HOH
1234
A
HOH
1235
4
HOH
HOH
1235
A
HOH
1236
4
HOH
HOH
1236
A
HOH
1237
4
HOH
HOH
1237
A
HOH
1238
4
HOH
HOH
1238
A
HOH
1239
4
HOH
HOH
1239
A
HOH
1240
4
HOH
HOH
1240
A
HOH
1241
4
HOH
HOH
1241
A
HOH
1242
4
HOH
HOH
1242
A
HOH
1243
4
HOH
HOH
1243
A
HOH
1244
4
HOH
HOH
1244
A
HOH
1245
4
HOH
HOH
1245
A
HOH
1246
4
HOH
HOH
1246
A
HOH
1247
4
HOH
HOH
1247
A
HOH
1248
4
HOH
HOH
1248
A
HOH
1249
4
HOH
HOH
1249
A
n
1
804
A
n
2
805
A
n
3
806
A
n
4
807
A
n
5
808
A
n
6
809
A
n
7
810
A
n
8
811
A
n
9
812
A
n
10
813
A
n
11
814
A
CYS
815
n
12
CYS
815
A
GLU
816
n
13
GLU
816
A
ARG
817
n
14
ARG
817
A
LEU
818
n
15
LEU
818
A
PRO
819
n
16
PRO
819
A
TYR
820
n
17
TYR
820
A
ASP
821
n
18
ASP
821
A
ALA
822
n
19
ALA
822
A
SER
823
n
20
SER
823
A
LYS
824
n
21
LYS
824
A
TRP
825
n
22
TRP
825
A
GLU
826
n
23
GLU
826
A
PHE
827
n
24
PHE
827
A
PRO
828
n
25
PRO
828
A
ARG
829
n
26
ARG
829
A
ASP
830
n
27
ASP
830
A
ARG
831
n
28
ARG
831
A
LEU
832
n
29
LEU
832
A
ASN
833
n
30
ASN
833
A
LEU
834
n
31
LEU
834
A
GLY
835
n
32
GLY
835
A
LYS
836
n
33
LYS
836
A
PRO
837
n
34
PRO
837
A
LEU
838
n
35
LEU
838
A
GLY
839
n
36
GLY
839
A
ARG
840
n
37
ARG
840
A
GLY
841
n
38
GLY
841
A
ALA
842
n
39
ALA
842
A
PHE
843
n
40
PHE
843
A
GLY
844
n
41
GLY
844
A
GLN
845
n
42
GLN
845
A
VAL
846
n
43
VAL
846
A
ILE
847
n
44
ILE
847
A
GLU
848
n
45
GLU
848
A
ALA
849
n
46
ALA
849
A
ASP
850
n
47
ASP
850
A
ALA
851
n
48
ALA
851
A
PHE
852
n
49
PHE
852
A
GLY
853
n
50
GLY
853
A
ILE
854
n
51
ILE
854
A
ASP
855
n
52
ASP
855
A
LYS
856
n
53
LYS
856
A
THR
857
n
54
THR
857
A
ALA
858
n
55
ALA
858
A
THR
859
n
56
THR
859
A
CSO
860
n
57
CSO
860
A
ARG
861
n
58
ARG
861
A
THR
862
n
59
THR
862
A
VAL
863
n
60
VAL
863
A
ALA
864
n
61
ALA
864
A
VAL
865
n
62
VAL
865
A
LYS
866
n
63
LYS
866
A
MET
867
n
64
MET
867
A
LEU
868
n
65
LEU
868
A
LYS
869
n
66
LYS
869
A
GLU
870
n
67
GLU
870
A
GLY
871
n
68
GLY
871
A
ALA
872
n
69
ALA
872
A
THR
873
n
70
THR
873
A
HIS
874
n
71
HIS
874
A
SER
875
n
72
SER
875
A
GLU
876
n
73
GLU
876
A
HIS
877
n
74
HIS
877
A
ARG
878
n
75
ARG
878
A
ALA
879
n
76
ALA
879
A
LEU
880
n
77
LEU
880
A
MET
881
n
78
MET
881
A
SER
882
n
79
SER
882
A
GLU
883
n
80
GLU
883
A
LEU
884
n
81
LEU
884
A
LYS
885
n
82
LYS
885
A
ILE
886
n
83
ILE
886
A
LEU
887
n
84
LEU
887
A
ILE
888
n
85
ILE
888
A
HIS
889
n
86
HIS
889
A
ILE
890
n
87
ILE
890
A
GLY
891
n
88
GLY
891
A
HIS
892
n
89
HIS
892
A
HIS
893
n
90
HIS
893
A
LEU
894
n
91
LEU
894
A
ASN
895
n
92
ASN
895
A
VAL
896
n
93
VAL
896
A
VAL
897
n
94
VAL
897
A
ASN
898
n
95
ASN
898
A
LEU
899
n
96
LEU
899
A
LEU
900
n
97
LEU
900
A
GLY
901
n
98
GLY
901
A
ALA
902
n
99
ALA
902
A
CYS
903
n
100
CYS
903
A
THR
904
n
101
THR
904
A
LYS
905
n
102
LYS
905
A
PRO
906
n
103
PRO
906
A
GLY
907
n
104
GLY
907
A
GLY
908
n
105
GLY
908
A
PRO
909
n
106
PRO
909
A
LEU
910
n
107
LEU
910
A
MET
911
n
108
MET
911
A
VAL
912
n
109
VAL
912
A
ILE
913
n
110
ILE
913
A
VAL
914
n
111
VAL
914
A
GLU
915
n
112
GLU
915
A
PHE
916
n
113
PHE
916
A
CYS
917
n
114
CYS
917
A
LYS
918
n
115
LYS
918
A
PHE
919
n
116
PHE
919
A
GLY
920
n
117
GLY
920
A
ASN
921
n
118
ASN
921
A
LEU
922
n
119
LEU
922
A
SER
923
n
120
SER
923
A
THR
924
n
121
THR
924
A
TYR
925
n
122
TYR
925
A
LEU
926
n
123
LEU
926
A
ARG
927
n
124
ARG
927
A
SER
928
n
125
SER
928
A
LYS
929
n
126
LYS
929
A
ARG
930
n
127
ARG
930
A
ASN
931
n
128
ASN
931
A
GLU
932
n
129
GLU
932
A
PHE
933
n
130
PHE
933
A
VAL
934
n
131
VAL
934
A
PRO
935
n
132
PRO
935
A
TYR
936
n
133
TYR
936
A
LYS
937
n
134
LYS
937
A
n
135
992
A
n
136
993
A
n
137
994
A
LYS
995
n
138
LYS
995
A
ASP
996
n
139
ASP
996
A
PHE
997
n
140
PHE
997
A
LEU
998
n
141
LEU
998
A
THR
999
n
142
THR
999
A
LEU
1000
n
143
LEU
1000
A
GLU
1001
n
144
GLU
1001
A
HIS
1002
n
145
HIS
1002
A
LEU
1003
n
146
LEU
1003
A
ILE
1004
n
147
ILE
1004
A
CSO
1005
n
148
CSO
1005
A
TYR
1006
n
149
TYR
1006
A
SER
1007
n
150
SER
1007
A
PHE
1008
n
151
PHE
1008
A
GLN
1009
n
152
GLN
1009
A
VAL
1010
n
153
VAL
1010
A
ALA
1011
n
154
ALA
1011
A
LYS
1012
n
155
LYS
1012
A
GLY
1013
n
156
GLY
1013
A
MET
1014
n
157
MET
1014
A
GLU
1015
n
158
GLU
1015
A
PHE
1016
n
159
PHE
1016
A
LEU
1017
n
160
LEU
1017
A
ALA
1018
n
161
ALA
1018
A
SER
1019
n
162
SER
1019
A
ARG
1020
n
163
ARG
1020
A
LYS
1021
n
164
LYS
1021
A
CSO
1022
n
165
CSO
1022
A
ILE
1023
n
166
ILE
1023
A
HIS
1024
n
167
HIS
1024
A
ARG
1025
n
168
ARG
1025
A
ASP
1026
n
169
ASP
1026
A
LEU
1027
n
170
LEU
1027
A
ALA
1028
n
171
ALA
1028
A
ALA
1029
n
172
ALA
1029
A
ARG
1030
n
173
ARG
1030
A
ASN
1031
n
174
ASN
1031
A
ILE
1032
n
175
ILE
1032
A
LEU
1033
n
176
LEU
1033
A
LEU
1034
n
177
LEU
1034
A
SER
1035
n
178
SER
1035
A
GLU
1036
n
179
GLU
1036
A
LYS
1037
n
180
LYS
1037
A
ASN
1038
n
181
ASN
1038
A
VAL
1039
n
182
VAL
1039
A
VAL
1040
n
183
VAL
1040
A
LYS
1041
n
184
LYS
1041
A
ILE
1042
n
185
ILE
1042
A
CSO
1043
n
186
CSO
1043
A
ASP
1044
n
187
ASP
1044
A
n
188
1045
A
n
189
1046
A
LEU
1047
n
190
LEU
1047
A
ALA
1048
n
191
ALA
1048
A
ARG
1049
n
192
ARG
1049
A
ASP
1050
n
193
ASP
1050
A
ILE
1051
n
194
ILE
1051
A
TYR
1052
n
195
TYR
1052
A
LYS
1053
n
196
LYS
1053
A
n
197
1054
A
n
198
1055
A
n
199
1056
A
n
200
1057
A
n
201
1058
A
n
202
1059
A
n
203
1060
A
n
204
1061
A
n
205
1062
A
n
206
1063
A
n
207
1064
A
n
208
1065
A
PRO
1066
n
209
PRO
1066
A
LEU
1067
n
210
LEU
1067
A
LYS
1068
n
211
LYS
1068
A
TRP
1069
n
212
TRP
1069
A
MET
1070
n
213
MET
1070
A
ALA
1071
n
214
ALA
1071
A
PRO
1072
n
215
PRO
1072
A
GLU
1073
n
216
GLU
1073
A
THR
1074
n
217
THR
1074
A
ILE
1075
n
218
ILE
1075
A
PHE
1076
n
219
PHE
1076
A
ASP
1077
n
220
ASP
1077
A
ARG
1078
n
221
ARG
1078
A
VAL
1079
n
222
VAL
1079
A
TYR
1080
n
223
TYR
1080
A
THR
1081
n
224
THR
1081
A
ILE
1082
n
225
ILE
1082
A
GLN
1083
n
226
GLN
1083
A
SER
1084
n
227
SER
1084
A
ASP
1085
n
228
ASP
1085
A
VAL
1086
n
229
VAL
1086
A
TRP
1087
n
230
TRP
1087
A
SER
1088
n
231
SER
1088
A
PHE
1089
n
232
PHE
1089
A
GLY
1090
n
233
GLY
1090
A
VAL
1091
n
234
VAL
1091
A
LEU
1092
n
235
LEU
1092
A
LEU
1093
n
236
LEU
1093
A
TRP
1094
n
237
TRP
1094
A
GLU
1095
n
238
GLU
1095
A
ILE
1096
n
239
ILE
1096
A
PHE
1097
n
240
PHE
1097
A
SER
1098
n
241
SER
1098
A
LEU
1099
n
242
LEU
1099
A
GLY
1100
n
243
GLY
1100
A
ALA
1101
n
244
ALA
1101
A
SER
1102
n
245
SER
1102
A
PRO
1103
n
246
PRO
1103
A
TYR
1104
n
247
TYR
1104
A
PRO
1105
n
248
PRO
1105
A
GLY
1106
n
249
GLY
1106
A
VAL
1107
n
250
VAL
1107
A
LYS
1108
n
251
LYS
1108
A
ILE
1109
n
252
ILE
1109
A
ASP
1110
n
253
ASP
1110
A
GLU
1111
n
254
GLU
1111
A
GLU
1112
n
255
GLU
1112
A
PHE
1113
n
256
PHE
1113
A
CSO
1114
n
257
CSO
1114
A
ARG
1115
n
258
ARG
1115
A
ARG
1116
n
259
ARG
1116
A
LEU
1117
n
260
LEU
1117
A
LYS
1118
n
261
LYS
1118
A
GLU
1119
n
262
GLU
1119
A
GLY
1120
n
263
GLY
1120
A
THR
1121
n
264
THR
1121
A
ARG
1122
n
265
ARG
1122
A
MET
1123
n
266
MET
1123
A
ARG
1124
n
267
ARG
1124
A
ALA
1125
n
268
ALA
1125
A
PRO
1126
n
269
PRO
1126
A
ASP
1127
n
270
ASP
1127
A
TYR
1128
n
271
TYR
1128
A
THR
1129
n
272
THR
1129
A
THR
1130
n
273
THR
1130
A
PRO
1131
n
274
PRO
1131
A
GLU
1132
n
275
GLU
1132
A
MET
1133
n
276
MET
1133
A
TYR
1134
n
277
TYR
1134
A
GLN
1135
n
278
GLN
1135
A
THR
1136
n
279
THR
1136
A
MET
1137
n
280
MET
1137
A
LEU
1138
n
281
LEU
1138
A
ASP
1139
n
282
ASP
1139
A
CYS
1140
n
283
CYS
1140
A
TRP
1141
n
284
TRP
1141
A
HIS
1142
n
285
HIS
1142
A
GLY
1143
n
286
GLY
1143
A
GLU
1144
n
287
GLU
1144
A
PRO
1145
n
288
PRO
1145
A
SER
1146
n
289
SER
1146
A
GLN
1147
n
290
GLN
1147
A
ARG
1148
n
291
ARG
1148
A
PRO
1149
n
292
PRO
1149
A
THR
1150
n
293
THR
1150
A
PHE
1151
n
294
PHE
1151
A
SER
1152
n
295
SER
1152
A
GLU
1153
n
296
GLU
1153
A
LEU
1154
n
297
LEU
1154
A
VAL
1155
n
298
VAL
1155
A
GLU
1156
n
299
GLU
1156
A
HIS
1157
n
300
HIS
1157
A
LEU
1158
n
301
LEU
1158
A
GLY
1159
n
302
GLY
1159
A
ASN
1160
n
303
ASN
1160
A
LEU
1161
n
304
LEU
1161
A
LEU
1162
n
305
LEU
1162
A
GLN
1163
n
306
GLN
1163
A
ALA
1164
n
307
ALA
1164
A
ASN
1165
n
308
ASN
1165
A
ALA
1166
n
309
ALA
1166
A
4.1475
0.5389
-1.0013
6.1376
-1.2638
7.2860
0.0290
0.0018
-0.1799
0.2230
-0.0372
-0.6185
0.5197
0.5172
0.0083
-0.3768
0.0389
-0.0285
-0.2480
0.0090
-0.2872
refined
16.9370
12.7380
5.7130
X-RAY DIFFRACTION
3.1188
1.3041
0.4963
6.5802
-4.0981
9.2842
-0.1294
0.0195
0.0933
0.4458
-0.0262
-0.2271
-0.8359
0.3453
0.1556
-0.1657
-0.0682
0.0062
-0.2143
0.0642
-0.2992
refined
11.1090
6.2430
32.6280
X-RAY DIFFRACTION
A
815
A
918
X-RAY DIFFRACTION
1
A
919
A
1166
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
1
monomeric
A
CSO
860
S-HYDROXYCYSTEINE
A
CSO
57
CYS
A
CSO
1005
S-HYDROXYCYSTEINE
A
CSO
148
CYS
A
CSO
1022
S-HYDROXYCYSTEINE
A
CSO
165
CYS
A
CSO
1043
S-HYDROXYCYSTEINE
A
CSO
186
CYS
A
CSO
1114
S-HYDROXYCYSTEINE
A
CSO
257
CYS
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLY
835
A
N
GLY
32
A
O
GLU
848
A
O
GLU
45
A
N
ILE
847
A
N
ILE
44
A
O
VAL
865
A
O
VAL
62
A
N
ALA
864
A
N
ALA
61
A
O
VAL
914
A
O
VAL
111
A
O
ILE
913
A
O
ILE
110
A
N
LEU
900
A
N
LEU
97
A
N
ILE
1023
A
N
ILE
166
A
O
ARG
1049
A
O
ARG
192
A
N
LEU
1033
A
N
LEU
176
A
O
LYS
1041
A
O
LYS
184
1
A
CG
GLU
816
A
CG
GLU
13
1
Y
1
A
CD
GLU
816
A
CD
GLU
13
1
Y
1
A
OE1
GLU
816
A
OE1
GLU
13
1
Y
1
A
OE2
GLU
816
A
OE2
GLU
13
1
Y
1
A
CG
ARG
840
A
CG
ARG
37
1
Y
1
A
CD
ARG
840
A
CD
ARG
37
1
Y
1
A
NE
ARG
840
A
NE
ARG
37
1
Y
1
A
CZ
ARG
840
A
CZ
ARG
37
1
Y
1
A
NH1
ARG
840
A
NH1
ARG
37
1
Y
1
A
NH2
ARG
840
A
NH2
ARG
37
1
Y
1
A
CG
PHE
843
A
CG
PHE
40
1
Y
1
A
CD1
PHE
843
A
CD1
PHE
40
1
Y
1
A
CD2
PHE
843
A
CD2
PHE
40
1
Y
1
A
CE1
PHE
843
A
CE1
PHE
40
1
Y
1
A
CE2
PHE
843
A
CE2
PHE
40
1
Y
1
A
CZ
PHE
843
A
CZ
PHE
40
1
Y
1
A
CG1
ILE
1051
A
CG1
ILE
194
1
Y
1
A
CG2
ILE
1051
A
CG2
ILE
194
1
Y
1
A
CD1
ILE
1051
A
CD1
ILE
194
1
Y
1
A
CG
TYR
1052
A
CG
TYR
195
1
Y
1
A
CD1
TYR
1052
A
CD1
TYR
195
1
Y
1
A
CD2
TYR
1052
A
CD2
TYR
195
1
Y
1
A
CE1
TYR
1052
A
CE1
TYR
195
1
Y
1
A
CE2
TYR
1052
A
CE2
TYR
195
1
Y
1
A
CZ
TYR
1052
A
CZ
TYR
195
1
Y
1
A
OH
TYR
1052
A
OH
TYR
195
1
Y
1
A
CG
LYS
1053
A
CG
LYS
196
1
Y
1
A
CD
LYS
1053
A
CD
LYS
196
1
Y
1
A
CE
LYS
1053
A
CE
LYS
196
1
Y
1
A
NZ
LYS
1053
A
NZ
LYS
196
1
Y
1
A
MET
804
A
MET
1
1
Y
1
A
ASP
805
A
ASP
2
1
Y
1
A
PRO
806
A
PRO
3
1
Y
1
A
ASP
807
A
ASP
4
1
Y
1
A
GLU
808
A
GLU
5
1
Y
1
A
LEU
809
A
LEU
6
1
Y
1
A
PRO
810
A
PRO
7
1
Y
1
A
LEU
811
A
LEU
8
1
Y
1
A
ASP
812
A
ASP
9
1
Y
1
A
GLU
813
A
GLU
10
1
Y
1
A
HIS
814
A
HIS
11
1
Y
1
A
ASP
992
A
ASP
135
1
Y
1
A
LEU
993
A
LEU
136
1
Y
1
A
TYR
994
A
TYR
137
1
Y
1
A
PHE
1045
A
PHE
188
1
Y
1
A
GLY
1046
A
GLY
189
1
Y
1
A
ASP
1054
A
ASP
197
1
Y
1
A
PRO
1055
A
PRO
198
1
Y
1
A
ASP
1056
A
ASP
199
1
Y
1
A
TYR
1057
A
TYR
200
1
Y
1
A
VAL
1058
A
VAL
201
1
Y
1
A
ARG
1059
A
ARG
202
1
Y
1
A
LYS
1060
A
LYS
203
1
Y
1
A
GLY
1061
A
GLY
204
1
Y
1
A
ASP
1062
A
ASP
205
1
Y
1
A
ALA
1063
A
ALA
206
1
Y
1
A
ARG
1064
A
ARG
207
1
Y
1
A
LEU
1065
A
LEU
208
1
Y
1
A
A
ALA
THR
872
873
-141.24
1
A
A
ILE
TYR
1051
1052
-148.22
1
A
ARG
817
A
164.05
-34.03
1
A
ARG
817
B
164.00
-28.77
1
A
ALA
842
-54.38
-2.14
1
A
LYS
856
A
73.87
-20.28
1
A
LYS
856
B
75.29
-5.40
1
A
LEU
868
-62.48
-164.73
1
A
GLU
870
-63.24
85.45
1
A
ALA
872
-124.50
-83.19
1
A
THR
873
5.78
128.78
1
A
ASP
1026
-155.72
63.55
1
A
ILE
1051
-55.29
97.01
62.689
2.38
0.00
0.00
0.72
0.00
-3.10
0.956
0.932
0.25813
0.20352
0.20518
2.15
34.92
601
17994
3.2
96.16
12.474
0.161
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.243
0.209
0.80
0.80
1.20
Unliganded Vegfr2 kinase domain solved in house - similar to pdb entry 1VR2
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.15
34.92
82
2361
50
0
2229
0.011
0.022
2401
0.001
0.020
1660
1.309
1.986
3250
0.896
3.000
4022
22.538
5.397
302
34.311
22.788
104
17.224
15.000
411
18.243
15.000
20
0.080
0.200
346
0.004
0.020
2678
0.002
0.020
511
0.225
0.200
475
0.191
0.200
1681
0.179
0.200
1158
0.086
0.200
1253
0.150
0.200
88
0.172
0.200
14
0.157
0.200
30
0.227
0.200
6
0.634
1.500
1490
0.127
1.500
579
1.002
2.000
2317
1.393
3.000
1067
2.072
4.500
933
0.324
0.264
2.210
34
948
20
69.50
43.5
2.15
40.
3CJF
18647
18596
-3
0.
0.042
1
42.4
6.6
96.3
0.423
2.15
2.23
2.3
1
74.3
refinement
REFMAC
5.2.0019
data collection
MAR345
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
AMoRE
Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
ASP
821
A
ASP
18
HELX_P
A
GLU
826
A
GLU
23
1
1
6
A
PRO
828
A
PRO
25
HELX_P
A
ASP
830
A
ASP
27
5
2
3
A
THR
873
A
THR
70
HELX_P
A
GLY
891
A
GLY
88
1
3
19
A
ASN
921
A
ASN
118
HELX_P
A
LYS
929
A
LYS
126
1
4
9
A
THR
999
A
THR
142
HELX_P
A
ARG
1020
A
ARG
163
1
5
22
A
ALA
1028
A
ALA
171
HELX_P
A
ARG
1030
A
ARG
173
5
6
3
A
PRO
1066
A
PRO
209
HELX_P
A
MET
1070
A
MET
213
5
7
5
A
ALA
1071
A
ALA
214
HELX_P
A
ARG
1078
A
ARG
221
1
8
8
A
THR
1081
A
THR
224
HELX_P
A
SER
1098
A
SER
241
1
9
18
A
ASP
1110
A
ASP
253
HELX_P
A
GLY
1120
A
GLY
263
1
10
11
A
THR
1130
A
THR
273
HELX_P
A
TRP
1141
A
TRP
284
1
11
12
A
GLU
1144
A
GLU
287
HELX_P
A
ARG
1148
A
ARG
291
5
12
5
A
THR
1150
A
THR
293
HELX_P
A
ALA
1166
A
ALA
309
1
13
17
covale
1.333
both
A
A
THR
859
A
C
THR
56
1_555
A
CSO
860
A
N
CSO
57
1_555
covale
1.335
both
B
A
THR
859
A
C
THR
56
1_555
A
CSO
860
A
N
CSO
57
1_555
covale
1.333
both
A
A
A
CSO
860
A
C
CSO
57
1_555
A
ARG
861
A
N
ARG
58
1_555
covale
1.337
both
B
B
A
CSO
860
A
C
CSO
57
1_555
A
ARG
861
A
N
ARG
58
1_555
covale
1.336
both
A
ILE
1004
A
C
ILE
147
1_555
A
CSO
1005
A
N
CSO
148
1_555
covale
1.330
both
A
CSO
1005
A
C
CSO
148
1_555
A
TYR
1006
A
N
TYR
149
1_555
covale
1.332
both
A
LYS
1021
A
C
LYS
164
1_555
A
CSO
1022
A
N
CSO
165
1_555
covale
1.325
both
A
CSO
1022
A
C
CSO
165
1_555
A
ILE
1023
A
N
ILE
166
1_555
covale
1.332
both
A
ILE
1042
A
C
ILE
185
1_555
A
CSO
1043
A
N
CSO
186
1_555
covale
1.331
both
A
CSO
1043
A
C
CSO
186
1_555
A
ASP
1044
A
N
ASP
187
1_555
covale
1.333
both
A
PHE
1113
A
C
PHE
256
1_555
A
CSO
1114
A
N
CSO
257
1_555
covale
1.336
both
A
CSO
1114
A
C
CSO
257
1_555
A
ARG
1115
A
N
ARG
258
1_555
TRANSFERASE
Vascular endothelial growth factor receptor 2. vegfr-2, kinase insert domain receptor, protein-tyrosine kinase receptor flk-1, Angiogenesis, ATP-binding, Developmental protein, Differentiation, Glycoprotein, Host-virus interaction, Immunoglobulin domain, Membrane, Nucleotide-binding, Phosphoprotein, Transferase, Transmembrane, Tyrosine-protein kinase
VGFR2_HUMAN
UNP
1
806
P35968
MDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSE
LKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYK
VGFR2_HUMAN
UNP
1
994
P35968
DLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMA
PETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTF
SELVEHLGNLLQANA
806
939
3CJF
804
937
P35968
A
1
1
134
994
1168
3CJF
992
1166
P35968
A
2
135
309
1
LYS
See remark 999
ASN
833
3CJF
A
P35968
UNP
835
30
5
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
832
A
LEU
29
A
ARG
840
A
ARG
37
A
GLN
845
A
GLN
42
A
PHE
852
A
PHE
49
A
CSO
860
A
CSO
57
A
MET
867
A
MET
64
A
MET
911
A
MET
108
A
GLU
915
A
GLU
112
A
LEU
899
A
LEU
96
A
CYS
903
A
CYS
100
A
ILE
1023
A
ILE
166
A
HIS
1024
A
HIS
167
A
ALA
1048
A
ALA
191
A
ARG
1049
A
ARG
192
A
ILE
1032
A
ILE
175
A
LEU
1034
A
LEU
177
A
VAL
1040
A
VAL
183
A
ILE
1042
A
ILE
185
BINDING SITE FOR RESIDUE SO4 A 1
A
SO4
1
Software
5
BINDING SITE FOR RESIDUE SO4 A 2
A
SO4
2
Software
2
BINDING SITE FOR RESIDUE SO4 A 3
A
SO4
3
Software
3
BINDING SITE FOR RESIDUE SO4 A 4
A
SO4
4
Software
3
BINDING SITE FOR RESIDUE SAV A1167
Software
9
A
LYS
824
A
LYS
21
5
1_555
A
GLU
826
A
GLU
23
5
1_555
A
PHE
827
A
PHE
24
5
1_555
A
ILE
854
A
ILE
51
5
1_555
A
LEU
900
A
LEU
97
5
1_555
A
ARG
930
A
ARG
127
2
1_555
A
SER
1102
A
SER
245
2
1_555
A
HIS
874
A
HIS
71
3
2_655
A
ARG
1116
A
ARG
259
3
1_555
A
THR
1121
A
THR
264
3
1_555
A
HIS
889
A
HIS
86
3
1_555
A
ARG
1020
A
ARG
163
3
1_555
A
ARG
1124
A
ARG
267
3
2_554
A
LEU
838
A
LEU
35
9
1_555
A
VAL
846
A
VAL
43
9
1_555
A
ALA
864
A
ALA
61
9
1_555
A
GLU
915
A
GLU
112
9
1_555
A
PHE
916
A
PHE
113
9
1_555
A
CYS
917
A
CYS
114
9
1_555
A
LYS
918
A
LYS
115
9
1_555
A
LEU
1033
A
LEU
176
9
1_555
A
CSO
1043
A
CSO
186
9
1_555
19
P 21 21 21